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[174272_at] S. pombe double-strand-break repair protein, RAD21

Description C56593_rc /REP_DB=TREMBL Accession /GB=C56593 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk264c9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 26      4grp_highest_8_8 > 43      4grp_high_8_8 > 48      6grp_highest_nonorm > 60      6grp_total > 27      4grp_total > 55      6grp_highest_sub > Cu      6grp_cgc > 04      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 368
1 2 3 4 range
A 565.6
(3)
P 		293.4
(-1.4)
P 		361.9
(-0.3)
P 		197.2
(-3)
P 		368
B 437.6
(3)
P 		329.2
(-3)
P 		368.6
(-0.8)
P 		335.6
(-2.6)
P 		108
C 360.9
(3)
P 		222.3
(-3)
P 		286.9
(-0.2)
P 		323.6
(1.4)
P 		139
avr 454.7
(3) 		281.6
(-3) 		339.1
(-1) 		285.5
(-2.9) 		173

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 370
1 2 3 4 5 6 range
A 514.2
(3)
P 		479.1
(2.1)
P 		295.2
(-2.7)
P 		284.2
(-3)
P 		430.8
(0.8)
P 		408.5
(0.2)
P 		230
B 444.9
(2.4)
P 		474.7
(3)
P 		267.8
(-1.5)
P 		250.8
(-1.8)
P 		197.2
(-3)
P 		308.5
(-0.6)
P 		278
C 566.7
(3)
P 		377.2
(-1)
P 		279.7
(-3)
P 		313.6
(-2.3)
P 		286.9
(-2.8)
P 		343.2
(-1.7)
P 		287
avr 508.6
(3) 		443.7
(1.3) 		280.9
(-3) 		282.9
(-2.9) 		305
(-2.4) 		353.4
(-1.1) 		228
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 177
1 2 3 4 range
A 205.9
(3)
P 		63.7
(-1.8)
P 		94.6
(-0.8)
P 		28.9
(-3)
P 		177
B 139.6
(3)
P 		81.3
(-2.1)
P 		85.4
(-1.8)
P 		71.5
(-3)
P 		68
C 119.5
(3)
P 		63.9
(-2.1)
P 		100
(1.2)
P 		54.6
(-3)
P 		65
avr 155
(3) 		69.6
(-2) 		93.3
(-0.6) 		51.7
(-3) 		103

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 147
1 2 3 4 5 6 range
A 94.8
(-1.3)
P 		170.4
(3)
P 		64.3
(-3)
P 		72.1
(-2.6)
P 		130
(0.7)
P 		99.5
(-1)
P 		106
B 154.8
(2.8)
P 		158
(3)
P 		65
(-3)
P 		66.4
(-2.9)
P 		80.1
(-2)
P 		115.1
(0.2)
P 		93
C 210.1
(3)
P 		115.1
(-0.9)
P 		71.2
(-2.7)
P 		63.1
(-3)
P 		92.8
(-1.8)
P 		114.9
(-0.9)
P 		147
avr 153.2
(3) 		147.8
(2.6) 		66.8
(-3) 		67.2
(-3) 		101
(-0.6) 		109.8
(-0) 		86
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174272_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22210
Sequence Type Exemplar sequence
Representative Public ID C56593 NCBI
Target Description C56593_rc /REP_DB=TREMBL Accession /GB=C56593 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk264c9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_076861(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076861 NCBI Caenorhabditis elegans COHesin family member (coh-1) (coh-1) mRNA, complete cds. 11/11 None
K08A8.3 ENSEMBL cdna:known chromosome:CEL140:X:7465199:7475239:-1 gene:K08A8.3 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:7465207-7465499(-) 100.0 100.0
Public Domain and Genome References
Gene Title S. pombe double-strand-break repair protein, RAD21
Gene Symbol coh-1
Ensembl K08A8.3
Entrez Gene 181003 Entrez gene
SwissProt Q21306 EMBL-EBI
WormBase CE04726 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1604145_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFA.1703.1.A1_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFA.19873.1.S1_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFA.20666.1.S1_S_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFA.21550.1.S1_S_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFAAFFX.2157.1.S1_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CHICKEN:GGA.4474.1.S1_S_AT RAD21 homolog (S. pombe) gga
CHICKEN:GGA.20047.1.S1_AT Similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) gga
HG-U133_PLUS_2:200608_S_AT RAD21 homolog (S. pombe) hs
HG-U133A:200608_S_AT RAD21 homolog (S. pombe) hs
HG-FOCUS:200608_S_AT RAD21 homolog (S. pombe) hs
HG-U133A_2:200608_S_AT RAD21 homolog (S. pombe) hs
HG-U133_PLUS_2:200607_S_AT RAD21 homolog (S. pombe) hs
HG-U133A_2:200607_S_AT RAD21 homolog (S. pombe) hs
HG-U133A:200607_S_AT RAD21 homolog (S. pombe) hs
HU35KSUBD:RC_AA287642_S_AT RAD21 homolog (S. pombe) hs
HUGENEFL:D38551_AT RAD21 homolog (S. pombe) hs
U133_X3P:G5453993_3P_A_AT RAD21 homolog (S. pombe) hs
U133_X3P:HS.81848.0.S1_3P_A_AT RAD21 homolog (S. pombe) hs
HG-U95AV2:38114_AT RAD21 homolog (S. pombe) hs
U133_X3P:HS2.424244.1.S1_3P_AT RAD21 homolog (S. pombe) hs
HG-U133_PLUS_2:1560207_AT RAD21 homolog (S. pombe) hs
MOE430A:1416162_AT RAD21 homolog (S. pombe) mm
MOUSE430_2:1416162_AT RAD21 homolog (S. pombe) mm
MOUSE430A_2:1416162_AT RAD21 homolog (S. pombe) mm
MOUSE430_2:1416161_AT RAD21 homolog (S. pombe) mm
MOE430A:1416161_AT RAD21 homolog (S. pombe) mm
MOUSE430A_2:1416161_AT RAD21 homolog (S. pombe) mm
MG-U74AV2:94768_AT RAD21 homolog (S. pombe) mm
MOUSE430_2:1455938_X_AT RAD21 homolog (S. pombe) mm
MOUSE430A_2:1455938_X_AT RAD21 homolog (S. pombe) mm
MOE430A:1455938_X_AT RAD21 homolog (S. pombe) mm
MU11KSUBA:D37790_S_AT RAD21 homolog (S. pombe) mm
MU11KSUBB:MSA.1791.0_I_AT RAD21 homolog (S. pombe) mm
MU19KSUBB:TC33672_AT RAD21 homolog (S. pombe) (Rad21), mRNA mm
RG-U34C:RC_AI231313_AT similar to HR21spA rn
RAE230A:1388504_AT similar to HR21spA rn
RAT230_2:1388504_AT similar to HR21spA rn
RAE230B:1382823_AT Similar to HR21spA rn
RAT230_2:1382823_AT Similar to HR21spA rn
RG-U34B:RC_AI070008_AT Similar to HR21spA rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7001 chromosome organization and biogenesis (sensu Eukaryota) inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
228 nuclear chromosome inferred from electronic annotation QuickGO AmiGO
5634 nucleus inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3684 damaged DNA binding inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA79748 Cohesin family protein 1 [Caenorhabditis elegans] ref|NP_509262.1| COHesin family member (coh-1) [Caenorhabditis elegans] 0.0
blast CAE70217 Hypothetical protein CBG16697 [Caenorhabditis briggsae] 0.0
blast XP_861017 PREDICTED: similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) isoform 3 [Canis familiaris] 1.0E-55
Protein Domains
Database ID Description E-Value
Pfam IPR006910 EMBL-EBI Rad21/Rec8 like protein, N-terminal 1.3E-59
Pfam IPR006909 EMBL-EBI Rad21/Rec8 like protein, C-terminal 8.4E-26
Sequence
Target Sequence 
>C. ELEGANS:174272_AT
aattcattatttccacttgtagtctacataatatttttaatcaacctcccattatttaat
ttatgctttatgttagaaaactttttattgccaacaatctctgaaaatttatcattccct
tcttgaaaagccactccacttttttacaacttctctccctccccccactatatcttatta
catgtttcccgccaaaattggtacagttcggttattgtcaacaagaaattgtgagatcac
taccagaactg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATTCATTATTTCCACTTGTAGTCT 78 177 24 Antisense
ATATTTTTAATCAACCTCCCATTAT 336 19 54 Antisense
AACCTCCCATTATTTAATTTATGCT 416 145 66 Antisense
TATTGCCAACAATCTCTGAAAATTT 91 665 109 Antisense
GAAAATTTATCATTCCCTTCTTGAA 589 353 126 Antisense
CTTCTTGAAAAGCCACTCCACTTTT 120 221 142 Antisense
TCCCCCCACTATATCTTATTACATG 649 595 183 Antisense
TTATTACATGTTTCCCGCCAAAATT 404 677 198 Antisense
TTCCCGCCAAAATTGGTACAGTTCG 535 695 209 Antisense
GGTACAGTTCGGTTATTGTCAACAA 168 505 223 Antisense
AATTGTGAGATCACTACCAGAACTG 141 179 250 Antisense
Sequence Source Affymetrix Proprietary Database